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GeneBe

rs1801260

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004898(CLOCK):c.*213T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152032 control chromosomes in the gnomAD Genomes database, including 4955 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 4955 hom., cov: 32)

Consequence

CLOCK
NM_004898 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.802

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CLOCKNM_004898.4 linkuse as main transcriptc.*213T>C 3_prime_UTR_variant 23/23 ENST00000513440.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLOCKENST00000513440.6 linkuse as main transcriptc.*213T>C 3_prime_UTR_variant 23/231 NM_004898.4 P1

Frequencies

GnomAD3 genomes
AF:
0.246
AC:
37470
AN:
152032
Hom.:
4955
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.172
Gnomad AMI
AF:
0.270
Gnomad AMR
AF:
0.233
Gnomad ASJ
AF:
0.236
Gnomad EAS
AF:
0.0993
Gnomad SAS
AF:
0.370
Gnomad FIN
AF:
0.356
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.280
Gnomad OTH
AF:
0.246
GnomAD4 exome
AF:
0.272
AC:
118169
AN:
435170
Hom.:
16931
AF XY:
0.278
AC XY:
63693
AN XY:
229406
show subpopulations
Gnomad4 AFR exome
AF:
0.179
Gnomad4 AMR exome
AF:
0.218
Gnomad4 ASJ exome
AF:
0.231
Gnomad4 EAS exome
AF:
0.130
Gnomad4 SAS exome
AF:
0.359
Gnomad4 FIN exome
AF:
0.339
Gnomad4 NFE exome
AF:
0.276
Gnomad4 OTH exome
AF:
0.260
Alfa
AF:
0.268
Hom.:
9691
Bravo
AF:
0.226
Asia WGS
AF:
0.261
AC:
908
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
Cadd
Benign
9.2
Dann
Benign
0.71
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1801260; hg19: chr4-56301369; COSMIC: COSV59401751;